AMBER Archive (2004)

Subject: Re: AMBER: Dummy torsion paramters for thermodynamic integration

From: David A. Case (
Date: Tue Dec 21 2004 - 09:49:29 CST

On Tue, Dec 21, 2004, Thomas Steinbrecher wrote:
> Is this error still relevant if I perform my TI runs with
> sander instead off gibbs? If not can I turn it off to be
> able to write my top files without these lines?

The warning is relevant to both sander and gibbs.

> When I add the dummy parameters requested, even after
> removing duplicate ones, ca. 30 entries remain for my
> .frcmod file. When I load these, I get another warning:
> -----
> WARNING: expected Improper Torsion PK>0 (0.000000)
> WARNING: expected Improper Torsion PHASE=180 (0.000000)

These are just warnings: since you have a force constant of 0, it doesn't
really matter that the phase is not 180 (which it should be for a real
improper). In the past, someone thought it was important to notify the
user when they were entering dummy parameters (with PK=0), but this may be
oversolicitous. But you can just ignore these messages.

...good luck....happy holidays!....dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to